


Lieutenant Colonel John Sheppard, United States Air Force, Military Commander, Atlantis Expedition, Pegasus Galaxy

by BainAduial



Series: First Times [2]
Category: Stargate Atlantis
Genre: F/M, Gen
Language: English
Status: Completed
Published: 2014-05-31
Updated: 2014-05-31
Packaged: 2018-01-27 17:18:08
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 9,591
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/1718399
Author URL: https://archiveofourown.org/users/BainAduial/pseuds/BainAduial
Summary: <blockquote class="userstuff">
              <p>The “First Times” series chronicles the pre-Atlantis lives of the expedition members, how they wound up in the Pegasus Galaxy, and some of the things they learned there. In this part, Lieutenant Colonel John Sheppard.</p>
            </blockquote>





	Lieutenant Colonel John Sheppard, United States Air Force, Military Commander, Atlantis Expedition, Pegasus Galaxy

**Author's Note:**

> AU for the events of episode 3x17 “Sunday”

John Sheppard doesn’t know why everyone always assumes he’s from a military family. Sure, his granddaddy served in the second World War, but he doesn’t know too many people who didn’t have relatives there. John’s first memory is of his momma putting his granddaddy’s cap and the jacket with the wings on the sleeves on him, and holding him over her head while he shrieks and makes airplane noises. The year is 1971, and the only thing in four-year-old Johnny’s world is his momma. She likes to tell him about his daddy, but daddy went off with someone called Uncle Sam to some place called Viet Nam, and daddy hasn’t come back yet.

~~~

John never does meet Uncle Sam, but when he’s six he and momma move in with her parents in northern California. Granddaddy took a few too many injuries in the war and gramma needs help taking care of him, and momma needs help too to take care of little Johnny, so it’s a good arrangement all around. The place they live isn’t quite big enough to be a city, but it isn’t quite small enough to be a town either. The street they live on is near the beach, and it’s a mix of retired folks and young families, so Johnny plays with the other kids while momma makes friends with the parents, and it’s sunny and happy and quiet, and even if by now Johnny’s realized that Uncle Sam and daddy aren’t ever coming home, well, he doesn’t remember them to miss them anyway.

~~~

Johnny’s friendly and outgoing and popular at school, and he thinks he’s mostly the same as everyone else. The first time he realizes he isn’t, he’s in the third grade being tested on multiplication, and he’s always been good with numbers, but apparently he’s better than good. Momma nearly bursts she’s so proud, and gramma just keeps grinning and saying ‘just like my Jonathan!’ while granddaddy fires numbers at him from the porch swing. Johnny, who still wears granddaddy’s flight jacket and cap, thinks being just like him is pretty much the best thing ever.

Two weeks later it’s John’s birthday and he gets to go to the local fairgrounds with his friends. They’re too little to ride everything, but John gets on the Ferris Wheel, and when it stops with him at the top he can see forever and he never wants to come down. It’s the first time little Johnny Sheppard ever figures out what it means to fly, and from then on, he’s hooked. He climbs every tree on the street, and his momma scolds him every time she catches him at it, because what if he fell?

~~~

The first time Johnny Sheppard learns what falling is like, he’s seven years old and one of his friends has dared him to pump the swing as high as it’ll go before jumping off. The rush of air about him as he goes is wonderful, and he’s laughing with joy when he hits the gravel, snapping his ankle in the wrong direction. The laughing continues through the howling as momma runs over, scared out of her wits and alternately scolding and hugging a battered little boy as he babbles about how totally groovy that was, and how he can’t wait to do it again. He keeps chattering until the adrenaline wears off, at which point he notices that his ankle really, really hurts, and starts crying. By then, momma’s gotten him to the hospital, and the doctor smiles and gives Johnny a lollipop and chatters with him about football while he examines the ankle, finally pronouncing it broken.

John ends up with a bulky plaster cast, a pair of crutches, and the admiration of everyone in his class, as well as something new to learn about while he’s cooped up recuperating – just what is this game football, anyway?

It takes little Johnny nearly two months before he’s cleared to start running around again, and during that time he spends a lot of Saturdays with his granddaddy on the couch, watching football games and daydreaming about being out on that field. Granddaddy chuckles, and ruffles his hair, and when Johnny’s finally allowed to go back to playing he’s presented with his first ever “authentic NFL pigskin” as granddaddy calls it. They go out to the yard to start playing catch, and when momma comes out to call them in for dinner she makes them pause in the yard for a minute while she snaps a picture with her new camera. When the film is developed, she buys a little silver frame for it and it rests in a place of honour on top of the mantelpiece in the living room, so everyone who comes in can admire it.

~~~

The first time Johnny Sheppard insists that his name is John, thank you, he has just turned ten and his granddaddy has said that this makes him a little man now. John’s so happy he could burst (and really, the massive chocolate cake has probably helped with that), especially when he gets his very own set of model fighter planes. Granddaddy calls him ‘my little pilot’, and teaches him all about the planes and their capabilities while they build and paint them on long winter evenings. Pretty soon there isn’t a room in the house that doesn’t have a model plane hanging from the ceiling, and momma laughs every time she has to duck under the one on the door to the laundry room.  
John says he’s going to take after his granddaddy and fly those planes someday, but all three adults pat him on the head and tell him he doesn’t have to, that he can be anything, go anywhere his little heart desires. He’s a good boy, and a good student (especially in math), and he’s all set to graduate from elementary school that spring and move on to middle school with the big kids. When he goes up at the graduating assembly, and grins at his momma with his front tooth missing, she’s got tears on her cheeks and the biggest smile he’s ever seen on her face, and he thinks she’s the prettiest momma ever.

~~~

Middle school’s a bit of a different experience for John. His elementary was really small, and everyone knew each other, but now there’s a few hundred kids running around and the teachers only teach one subject, and nobody here knows he’s special. Still, John’s a cute kid, not the biggest or most mature for his age but certainly not the littlest either, and he’s bright, and good at sports, and cheerful, and easygoing which not too many of his peers are, so he makes easy friends with everyone. They haven’t yet hit the age where cliques start to matter, so it’s okay that John sometimes imitates Mr. Spock while wearing his soccer uniform, or tells a joke that involves the characters of Battlestar Galactica.

~~~

John’s just turned fifteen and about to start the ninth grade – high school, and isn’t that a scary thought – when his world is turned upside down. Momma and gramma and granddaddy had been out for the evening at some sort of cultural event – John never cared to ask what, beyond making sure he wasn’t expected to go – and when it’s gone midnight and John’s still up watching reruns on television and waiting for them to come home, he starts to get a little worried. But when it goes on towards one in the morning, and a policeman shows up on his door and starts the conversation with 'I’ve got some bad news, son’, John really starts to panic.

He goes with the cop to the hospital, but it’s already too late, he knows it is. Still, he goes, and a few years later when it all settles in his head he’s glad he did, because he got a chance to say goodbye, and to hear his momma say she loved him and his granddaddy say he was proud of him and his gramma to say, as she always did, ‘so much like my Jonathan!’, and eventually that’ll mean something to him.

Now, though, he’s just fifteen, and everyone he loves is lying in the hospital morgue because of some asshole who went spinning around the winding coastal roads too fast after having several too many to drink, and nothing in John’s world is ever going to be quite all right again. He’s numb for a while, while the police help him go through the house and pack his things and whatever he either wants to take, or has been left to him in the wills, and the numbness doesn’t really start to wear off until he’s in the back of a car, clutching his granddaddy’s flight jacket at being driven into San Francisco to the nearest orphanage that’s got room for him.

After a couple of days, the numbness wears off and it’s replaced by anger – at his momma and grandparents, at the police, at the orphanage workers, at the other kids, but mostly at himself, because he wasn’t there. Wasn’t there to help them, although somewhere deep down inside he knows that there wasn’t anything he could’ve done except die right along with them. But still, he’s angry, and he’s fifteen, and so he takes it out on everyone. The new high school isn’t in the best area of town, and it tries hard, but it’s all too easy for John to fall in with the wrong crowd. The alcohol and the cigarettes are new, and all his friends are doing it, and if he starts missing more and more of his classes, and gets mouthier and mouthier to the teachers and social workers who try to intervene, well, that’s nobody’s business but his, is it?

At sixteen, somewhere in the middle of tenth grade, John’s headed straight for a career as a full-time drop out street punk (if he doesn’t end up in juvie hall or dead in a ditch somewhere) when the school’s old football coach retires, and a new coach is hired. Budget cuts mean that the new coach also ends up teaching most of the boy’s gym classes, but John hasn’t been to gym in months anyway, so he doesn’t know why this should affect him. Still, he goes, a few weeks after the guy’s started teaching, just to see what the fuss is all about. He’s pretty much indistinguishable from the rest of the boys on the field, in his shorts and school shirt, but something about his slouching attitude makes the teacher notice him. John thinks later that it’s probably the single moment that, if he were to blame the rest of his adult life on something he did as a child, this would be it.

The teacher asks his name, and John just shrugs, dropping his smoke and crushing it under his sneakers. The teacher’s back straightens with a snap, and all of a sudden John’s looking right at his granddaddy, forty years younger, in one of his rare moments of true anger. ‘Name, boy!’, the teacher barks out at full military bellow, and John unthinkingly snaps to attention himself, ‘John Sheppard, sir!’ spilling out before he can stop it. He’s disgusted with himself afterwards, of course, and he has a lot of time to contemplate why as the teacher makes him drop and give twenty, followed by singling him out of the class – the other boys are all going to play soccer – and making him run laps around the track. For some reason, John finds himself doing it instead of snorting and walking away, and his bad-boy reputation is forever crippled. 

After class, the teacher – Coach, and John starts calling him – takes John back to his office, and sits him down, and they have a good long talk about John’s attitude and John’s past and John’s future, which up until that point John hadn’t really been in any condition to worry about. Coach helps John clean up his act, tutors him so he can catch up in class, and even goes to bat for him with the principal so that John can be allowed to join the football team. The principle isn’t sure about giving a delinquent the chance to ruin the school’s good name, but Coach is persuasive, and in the end the principle gives in. He’s a little shocked, come the first game John plays in, when the skinny young man darts through opponents twice his weight to score the winning touchdown. 

The rest of the football team isn’t quite sure how to take it either, though they cautiously decide to accept the new kid, especially since he really is fast, and stronger than he looks, and kind of funny now that he’s opening up a bit. Still, he’s an outsider, and he was one of those no-good punks, and he never quite fits in.

John starts the eleventh grade in 1983, having just turned seventeen, and he’s determined to make his momma and granddaddy proud of him again. He lost track of that a bit, while he was hurting and angry, but he knows he can do it. He studies, and studies hard because somewhere along the lines of skipping class he’s managed to miss almost two years’ worth of material. Still, he’s smart and charming – a skill he perfects wheedling help out of his English teacher, a scary old librarian of a woman with a heart of gold – and before long he’s entirely caught up. Especially in math, where he’s been asked to join the school’s math league. He does, since it’s on a night he doesn’t have football practice, and for the first time in six years he manages to make a Star Trek joke and have people laugh at it (actually, it’s the first time in six years he’s made one, because he was afraid of being considered a dork). John’s happy, and adjusting to his life, and he’s finally back on track to being whatever he wants to be when he finishes, and he’s friendly and pleasant – if a little less open with his heart – and he’s dating one of the cheerleaders, a young lady who’s also on the debate team, and he’s got friends, even if they’re never as close as most other people’s, because the math geeks don’t really get the football team, and the football team doesn’t really get the math geeks, and nobody really gets his occasional tangents.

He spends a lot of time sitting in Coach’s office doing his homework, actually, and it’s there that he first hears the music of Johnny Cash. At first, John doesn’t really like it – he prefers Duran Duran, or Blondie, or sometimes the Beach Boys – but slowly the lyrics start to grow on him. He and coach have a lot of rambling discussions about Johnny Cash, and John doesn’t realize it, but between them Coach and the singer manage to shape a lot of his adult worldview. Even if he does still prefer to listen to “California Girls” while dancing around in his underpants in his room at the orphanage.

John keeps himself on the straight and narrow for another year, and a couple of months before his nineteenth birthday he somehow manages to graduate high school with honours. It’s a bit of a shock to suddenly be an adult with a diploma, especially as it means he has to find somewhere to go, because he’s legally an adult and a high school graduate, and thus no longer the responsibility of the State of California, which desperately needs more room in its orphanages. So John packs up his stuff, and somehow fits it all into the back of the beat-up old clunker he’d bought for practically nothing and fixed up in auto shop until she ran like a beauty, and he heads out of San Fran looking for whatever life’s going to hand him.

It doesn’t take more than a few weeks for John to realize that life’s not going to hand him much more than it ever has, and he finds a sleepy oceanfront town, a little old lady named Mrs. Phillips in need of a little extra income and with a basement quite to rent out, and a community college that’s pretty good in math and engineering. John rents the suite out, helps Mrs. Phillips with her chores, gets himself a job at the local burger joint, buys a surfboard, and gets ready to earn enough money to start putting himself through school.

~~~  
John finishes his first degree in three years, by taking courses in the summer. He’s been working solidly all that time, as well as helping Mrs. Phillips out and learning to surf, so he’s fit and tanned and he’s got a little bit of money under his belt and a bachelor’s degree in applied mathematics, and he decides it’s about time to move on before he becomes so entrenched that he doesn’t want to. In some ways, John’s still a little bit afraid of commitment, still running away from the things that make him happy.

So John sets out again, without any particular direction in mind, and somehow or other John ends up in the right place at the right time on the fourth of July to be riding a Ferris Wheel while the Air Force planes scream overhead in a stunning display of aerial manoeuvres, and John’s suddenly seven years old again and dreaming of flying. Only this time, he’s old enough and smart enough to know how to go about it. He winds up in a USAF recruitment office a few days later, ready to follow in his granddaddy’s footsteps and serve his country by flying high above her. He begins basic training in the spring of the year 1990, at the age of twenty-three.

~~~

The first time John thinks he may have made a mistake, one of his drill sergeants is screaming at a fellow cadet – not a future officer, like John signed up to be, but John doesn’t really care – about the cadet’s pathetic performance. John, who knows the kid from meals in the mess, and who knows that he’s having a rough time already – a horrible round of the flu, a break-up with his girlfriend, and the news from home that his grandfather was in the hospital – decided to tell the Sergeant exactly what he thought of the man’s teaching skills, with occasional digressions onto the subject of his parentage. Years late, John will be amazed that he escaped that incident with his commission intact and only a reprimand and a month’s worth of KP as punishment. 

However, John sticks it out, and finishes training, finally earning the right to call himself Second Lieutenant John Sheppard, USAF. He’s just in time to be deployed into the end of the Persian Gulf War, and John’s first tour of duty in the middle east gives him the beginnings of what will eventually become a solid, deep-seated hatred of the desert. He goes home after his first tour, and back into training, taking the time to earn his master’s degree in aeronautical engineering. He takes advantage of the time at home – since Colorado seems to be home now – to learn more about the aircraft that his branch of the service flies. On his second tour of duty, after being promoted to First Lieutenant, he’s a co-pilot in a helicopter, and John has finally learned how to fly.

Over the next several years, John matures a lot, makes new friends, and sees more of Africa than he ever really wanted to, interspersed with trips to various other hotspots. Eventually, he’s flown over – and set foot on – every single continent except for Antarctica, for one reason or another, and he’s flown nearly every helicopter the USAF employs. He celebrates his promotion to Captain in back in California, where he meets a lovely young blonde named Christine. She’s completely enamoured of his stories, and friendly and helpful and willing to write to him while he’s overseas, and before long he’s decided that, well, twenty-nine is quite old enough to be thinking about getting married. So he thinks about it, and decides that Christine’s nice, and pretty, and doesn’t seem to mind when he’s not around for long periods of time, so he proposes. It’s a small wedding, while he’s home on leave, and then he’s back in the air and leaving her to set up house in the Officer’s Housing on base, and he doesn’t really see any more of her than before.

The first time John gets a hint that this isn’t really working, he’s thirty-two and has just returned from a rather long test flight of his newly repaired helicopter. Christine’s waiting for him with a lawyer, and he signs the divorce papers to make her happy, a little surprised but a lot less upset than he really should be. But then, John Sheppard is good at saying goodbye. He’s a lot less good at letting people far enough in that he doesn’t want to, and Christine, for all that she was his wife, never quite made it there. He ponders, rather drunkenly while his friends Mitch and Dex attempt to get him to talk about it, that it’s just the way his life is going to be from then on: a string of surface friends and relationships that go nowhere. 

~~~

John goes back to his piloting and his duties, and he doesn’t think too much about it. He’s had a few more reprimands on his record, mostly about his attitude, because despite Coach’s best efforts John never quite managed to curb that slouching, laconic air that seems to drive certain of his superiors absolutely bonkers. John doesn’t really care. He’s a good pilot, and a good officer, and he cares about the men under his command and does his best to bring them all home safely whenever they’re deployed, and if it’s not quite the life he could have had, and if he occasionally sits in his bunk at night, alone in a foreign country with the bombs whistling overhead, and dreams of Mrs. Phillip’s basement suite and a job – maybe as a teacher, or a waiter, or any number of other simple, homey things – and summers full of sand and sun and surfing, well, he doesn’t think his life turned out that badly. And besides, what he’s doing makes it possible for other people to enjoy that life, people with loved ones and friends who deserve it more than he does.

John is thirty-four years old when, during one of his periods of leave in the States, two hijacked planes crash into the Twin Towers in New York. John, like the rest of his country, is in shock. He’s not too far away – visiting Mitch, who’s on medical leave at home in New Jersey – so he goes to help, his uniform letting him in to what they’re calling ground zero. John’s seen battle, and he’s seen death, but he’s never seen anything like this. No one has, he supposes, and they’re all a little shell-shocked as they keep pulling survivors out of the wreckage, until there aren’t any more survivors and they’re just pulling bodies, but still they can’t stop. 

That particular set of actions earns John a commendation, almost enough to wipe out all his previous reprimands, and his leave is extended for a couple of months. When he goes back to active duty, it’s as a Major, although John would really rather have missed the promotion if it’d mean that the entire several months were just a bad dream and he can wake up now. But they weren’t, and his country’s at war. This is a different kind of war than the ones he’s been in before, potentially endless, with a lot more emotion invested in it on all sides, and John doesn’t like it. But he offered Uncle Sam his twenty years of service, just like his granddaddy and his daddy did back in their day, and he’s got no way out of it now. So John goes, in the year 2002, to Afghanistan. And John flies in supplies and personnel, and John does all the things a helicopter pilot in the service of the USAF is supposed to do, and he takes care of his men, and he raises morale with a joke whenever he can, and he’s impressed as always by the spirit people can put forward in a situation like that. Because it’s hot and dusty and far from home, and people are dying and bombs are falling until the warning siren becomes just another nightly occurrence, but somehow they all band together and bear up under the pressure, celebrating the little things like his bunkmate’s daughter being born – apparently they’d named the little bit Hope – and one of the lieutenant’s sisters’ marriage (despite the fact that none of them had ever met the girl). 

~~~

The first time John Sheppard disobeys a direct order, it is in the fall of 2002, and Mitch and Dex are dead, and Captain Holland is shot down. John goes after him, because you don’t leave a man down in enemy territory, not if there’s a chance of getting him out. You just don’t. But John’s too late, and Holland’s dead too, and then John’s back Stateside and facing a disciplinary hearing. They won’t drum him out of the service, not over this, and they won’t demote him, if only because of his actions in New York, but they suggest he might like a less stressful posting. John, heartsick and tired and wondering for the thousandth time in recent years why he joined the Air Force instead of becoming a commercial pilot flying surf bums around California, agrees with them. 

So now John’s in Antarctica, and it’s colder than anywhere he’s ever been in his life. But it’s also quiet, and peaceful, and he doesn’t have to do much other than ferry supplies out to some sort of research base every few days. So he does a lot of reading, and a lot of listening to music – to his surprise, Johnny Cash now sounds better than Duran Duran, although the Beach Boys are still better than either – and generally decompressing. He knows he’ll be here until he retires, but really, that’s sort of okay with him at this point. He settles into a rut, and life keeps chugging along its merry way.

~~~

The first time John Sheppard is shot at by alien artillery, he is flying a visiting General out to the research base. John hasn’t asked what a research base needs with a General, but when he’s sharply ordered not to ask about the weapon that nearly blew them both out of the sky, he gets the idea that there’s more going on down here than he really wants to know about. So he keeps quiet, and follows the General down into the bowels of the research station, where they’re met by a chubby, sarcastic son-of-a-bitch wearing a bright orange pullover and a no-nonsense woman in red. They all seem to know each other, and then they’re off to meet with someone called Dr. Jackson, who reminds John a little bit of a puppy dog, but one with teeth. Sharp teeth. He thinks that, as he’s not General O’Neill, he’ll just as soon stay out of the good doctor’s way. So he goes looking around, following the General’s strict orders not to touch anything, until he finds a Scottish man gleefully describing something or other to do with the weapon that he was sure would kill him.  
Half of a confusing conversation later, he’s in some sort of glowy chair and there are planets rotating around his head, and the only thing he can think to say is ‘did I do that?’.

~~~

The first time John Sheppard steps through a wormhole to another galaxy, it’s after a month or so of the most confusing, eye-opening meeting he’s ever sat through, accompanied by a coin toss while sitting on the grass back in San Francisco, where he’s gone to spend his last few days on earth. What a strange concept. John isn’t really sure, up until he’s examining his belongings in those last few days, what he’ll take with him. Apart from the sporting equipment that he’s had in storage for years, he doesn’t own much – the military lifestyle doesn’t lend itself to gathering clutter. He finally settles on two things. The old black-and-white photo of himself and granddaddy and the football, and a Johnny Cash poster Coach gave him for graduation. There’s nothing else that really means much to him, anymore. And so, armed with Johnny Cash and the memories of his family, John Sheppard sets out to explore strange new worlds, to seek out new life and new civilizations, to boldly go where no man has gone before, and to hopefully not piss his new commanding officer off too badly the first day.

He succeeds at two out of the three, which isn’t bad, in his books. He finds strange new worlds, and new life and new civilizations, but Colonel Sumner doesn’t like him much at all. But, well, Colonel Sumner doesn’t really have much time to revise that opinion before John has to perform a mercy killing, the first time he’s killed one of his own men, the first time he’s killed at all since being shipped home with a black mark on his record. It’s surprisingly easy to go back to, but John knows that once the adrenaline of battle has worn off, he’ll be hurling up his lunch in private.

But then John’s woken the Wraith up, and that’s bad. It’s very bad. It’s so bad John doesn’t have words for the badness of it. And suddenly John’s in charge of the safety and security of a whole bunch of civilians who have no training to deal with any of this – not that the Air Force Academy exactly had classes in dealing with armadas of life-sucking alien catfish with leather fetishes in another galaxy – and a whole bunch of eager young military personnel from branches of the service he’s never had much to do with, if they’re even from the United States, and not everyone speaks English, and not everyone gets along, and somehow, he’s got to keep them alive. Because they’re his now, in a way no one ever has been before.

So he forms a gate team, in the tradition of the earthly SGC, and he heads out into the unknown with an alien diplomat, a panicking hypochondriac Canadian astrophysicist, and a spunky young Marine Lieutenant with far more energy than John remembers having at his age. He thinks, the first time they step through the wormhole, that if they ever end up saving the galaxy, it’ll probably be by accident.

As if the Wraith weren’t bad enough, John quickly comes to believe that the Ancients were either suicidally irresponsible or some of the worst examples of ‘book sense, not common sense’ that he’d ever seen. Because really? How many dangerous experiments can one race possibly leave lying around without instruction manuals, or any kind of guide to what they are and what they do and why they exist?

Apparently, a great many. But John doesn’t have to deal with most of them. He just has to deal with things like giant mosquitoes leeching onto his neck and trying to suck out his blood. Which, okay, is probably good for one or two vampire jokes, but really not so much fun. Especially the part where he has to be shocked to death and thrown through the event horizon of an unstable wormhole minutes before it collapses. He doesn’t remember that part, of course, but there’s just no way in which that doesn’t suck, really.

John keeps going, though, through a number of subsequent adventures that include taking a Wraith prisoner and naming it – and one of these days, he’s really going to have to work on that annoying tendency he has to give things really flippant names – and things go well, like clearing Teyla of suspicion, and things go badly, like Hoff. But all in all, John’s mostly doing what he’s trained to do, which really puts him in the minority on this expedition. His life here – protecting the scientists – isn’t really that much different than his life in various war zones back home, although it is starting to run short of coffee, which no military base he’s ever served on ever has.

So John goes along like always, more free now to let his somewhat sarcastic edges out since there’s no one to reprimand him for it, and for the first time since he was a kid he starts almost fitting in. it actually reminds him a bit of high school, some days, since he doesn’t quite fit in with the military boys, being Air Force and their commanding officer, and he doesn’t quite fit in with the scientists, being military, but he somehow manages to get pretty friendly on a surface level with all of them. But now he’s got a group, a clique of his own, in the command team of Atlantis, and they’re all getting a lot closer than anyone ever has, especially Rodney, and isn’t that just a surprise to everyone involved. But the two of them get along well, for whatever reason, and John starts to not worry so much about what’s going to happen to them and to enjoy the life he’s been handed. Even when they meet the Genii and things go belly up, almost with nuclear weapons, life is pretty darned good for John Sheppard.

~~~

It can’t continue, of course. There’s a storm, and an evacuation and a hostile takeover, and then John’s raised the shield and killed sixty men. Okay, not quite sixty. But still. Those men were his enemy, yes, and John learned all about fanaticism in the deserts of the middle east, way back on earth, but they probably had families and homes, and it makes John sick that he’s capable of that kind of act. It saved his city and his people, yes, and he knows he’d do it again, but that doesn’t make it any easier. There’s a darkness to him, he thinks sometimes, that Dr. Weir will never understand no matter how long they know each other. He thinks Rodney sometimes understands it, although he doesn’t know why, and he knows the other military personnel and even some of the scientists – especially the ones from eastern Europe – understand, as well, but he’s the one in charge. Ultimately he’s responsible, both for every life lost amongst his on people and for every life taken from the enemy, and that’s a heavier burden than he ever thought it could be. After the storm’s gone, John wishes that strong liquor had been among the essential supplies brought from earth, but he figures it’s probably a good thing that it wasn’t.

Life goes on, Wraith and odd nano-virii aside, and shortly after John detonates a nuclear explosion above Atlantis using one of their precious naquaddah generators he’s having his first encounter with an alien priestess and Rodney McKay is making his first round of Captain Kirk jokes. John, who had despite his military service always liked just about all of the original crew better than Kirk, decided not to start squabbling over favorite Star Trek characters and went back to spending time with Chaya. Rodney turned out to be right, of course, and John felt a little better about not sleeping with her after he found out she was really an Ancient – and he’s getting back into the realm of ‘how did these guys become the most advanced race in the universe’ again, but that’s a subject for another time – and then he’s having some weird glowing melding experience that he’s not really sure how to describe. It leaves him relaxed, anyway, and a little more open to friendship than he used to be, if a little warier of alien women, and he goes back to letting life pass as it will.

So, there are adventures, and friendly aliens, and not so friendly aliens, and strange alien plant life, and strange alien animals that look like dinosaurs, and strange alien priesthoods, and Genii (and Sheppard is really starting to think that a good old fashioned vigilante killing is justified in Kolya’s case, but it’s a line he’s not quite ready to cross, because he doesn’t know what that would do to his already fairly shredded soul, so he leaves him alive. For now. Besides, there are more important things to do. Like go home – and it’s funny how quickly Atlantis has become home, when nowhere else ever really has been – and record messages to the families of the people he’s lost. He’s got none of his own to send, but those families deserve to know that their children died with honour (although he knows that that’s an empty phrase to a grieving parent) and that they are mourned by their friends. 

And then they’re under siege, and he’s suddenly under the command of yet another stiff, rule-thumping bastard like so many of the ones he’s run up against time and again over his years of service, and they’re fighting for their city and for earth. And then he’s taking a nuclear bomb on what he knows is a suicide mission, and he’s hoping to god that it works because he’d hate to have died for nothing, and then he’s standing on the bridge of an earth starship and watching as the Wraith hive goes up in a fiery explosion, and somehow they’re managing to hold their own. And then they’ve won, although he’s not really sure how, and they’re counting the losses. And the losses are high, and he’s not sure it was worth it, because they were all good men and women, many of them never trained to hold a weapon of any kind, and even those that were never deserved to die this far from home, fighting this kind of battle against an enemy that thought they were food. 

But they had. And even those that lived weren’t unscathed, many aged decades in a single moment, most just soul-sick from the things they’d seen, some with more mundane battlefield wounds, and Aiden Ford high on an enzyme that they couldn’t combat. And then Ford's gone and they’re on their way back to earth for the debriefing from Hell, and John’s sure he’s about to lose command of Atlantis, if not his posting there entirely, and he’s almost certain that that will be the final straw that breaks his back. Because nothing in his life has ever meant as much as the shining city and her people have come to mean to him.

John never expected to make it to Lieutenant Colonel. Especially after his stint in Afghanistan. So when General O’Neill pins the silver oak leaves onto his uniform, and gives him back everything he’d ever wanted in the form of official command of Atlantis, it’s the most surreal – and happy – day of his life. Well, not really. It’s overshadowed by a lot of things and John’s sure there were happier days, a long time ago, when he was a lot younger and a lot less battle-weary. But still, it’s amazing and shocking and everything he’s ever wanted and never knew he did, all rolled up into one. And John swears that he’ll do better this time. That fewer (preferably none) of his people will die anymore, and that somehow he’ll be able to keep them all safe while they explore the Pegasus Galaxy.

It’s a vain hope, of course. They don’t even make it all the way back to Atlantis before one of the scientists is dead and John and Rodney are pulling another hare-brained stunt at the last minute, chasing down a rogue fighter from the Daedalus through the coronosphere of a sun. Rodney panics about their prospects of ever having children, given the amount of radiation they’ve been exposed to, but John privately thinks that the likelihood of that – for either of them – was pretty small to begin with. But they get the fighter, and the make it back to Atlantis, and things settle down into the usual mess of short bursts of panic followed by long bursts of boredom. John’s determined to find Ford, so they’re out looking for him when they end up finding another alien, this one a soldier named Ronon Dex. John brings him home, and the look on Elizabeth’s face is rather like that of a kindergarten teacher faced with a young boy bringing in some exotic form of bug and asking to keep it, but she lets him try and settle Ronon into life on Atlantis. 

He succeeds, mostly because he pretty much lets Ronon do his own thing, he thinks. He’s never been a big believer into forcing people to do things just because he can. He’d rather let his men follow their own instincts, as long as they’re competent to do so. Ronon is definitely competent, and John has no reservations about letting him onto his off-world team. It somehow feels less like replacing Ford if it’s an alien taking his place, rather than another military officer. After that, there’s a brief interlude while McKay has a woman stuck in his head (and oh, the chuckles John got out of that in private after they were both safely back in their own bodies in the infirmary), and then it’s back to their usual round of chaotic missions and entertainingly bad first contact situations. John privately suspects that Teyla and Ronon think he and Rodney are kind of, well, dorky, but he doesn’t really mind. They’re not from earth, so he doesn’t have to try quite so hard to fit into the macho military stereotype around them.

So then McKay damages his trust a little bit (okay, a lot), and they have to work harder at their friendship, which is something John’s never done – both because he’s never trusted anybody quite that much, and because even if he had, he’d never have tried to get that level of it back after it was damaged with anyone else – and then he’s turning into a bug. Which, okay, the blue skin and stuff? Kind of cool, in a bad 1960s b-movie sort of way. But the running on instinct and trying to kiss Teyla (which would have been like kissing his sister, if he’d had a sister) and kill people? Not so cool, really. But they fix that, and then he gets to play in virtual reality on an old abandoned Ancient warship, which really reminds him of the episodes on Next Generation where things go wrong with the holodeck. Unfortunately, due to the interference of the Wraith, that analogy turns out all too accurate and he has to set the self-destruct on the ship. She was such a pretty ship, too!

After that, they find Ford. And he’s a little bit crazy – okay, he’s batshit insane. But John’s convinced they can get him back. Except they don’t. Although they do blow up a hive ship in the process. And McKay almost ends up addicted to the enzyme too, which John doesn’t even know about until they’re back on Atlantis, and he thinks that it’s a good thing Beckett managed to help McKay, because he doesn’t think he could stand to lose anyone else that way. 

~~~

The first time John Sheppard really gets a chance to sit back and think about his life, he’s on an alien planet. That isn’t really odd, considering what he does for a living. However, on this alien planet he’s been separated from his team, and after a few weeks, he’s determined that they aren’t coming for him. He doesn’t know why, and it’s a constant source of worry in the back of his mind. He ends up in a local village – the only local village, as far as he can tell – under the care of a trio of siblings, after rescuing the eldest and only boy from some kind of monster in the fields. They teach him to meditate – he keeps falling asleep, or thinking about Ferris Wheels, or any number of other things, really, so he’s not sure why they keep trying – and the girl seems like she’d like to have some kind of relationship with him. But John still has his walls that he won’t let down for just anybody, and even after several months have passed and he’s starting to acknowledge that for whatever reason, he probably will spend the rest of his life here, he can’t let those walls down for her. And she’s not the sort of girl you have a one-night stand with, so that’s the end of that. But he learns a lot from these people, whether he realizes it at the time or not. Most of it’s about how he views himself and the people around him, and a lot of it just has to do with spending a few months somewhere reasonably safe, with no bomb siren or gate-activation klaxons. It’s boring, but peaceful, and he thinks a few of the open wounds – the ones on the inside, where no one can see them bleeding – are finally closing during his time there.

He’s rescued, eventually, and when they explain that it was a time-dilation field and really only a couple of days has passed – not six months – he’s a little floored. He’s also six months older, whatever they have to say about it, and six months more introspective, but he keeps that to himself. So he goes back to Atlantis, and takes up command, and there are bomb threats and Go’a’uld spies, and John and Ronon are crossing a line of their own and threatening to torture one of their own people. When Kavanaugh turns out to be perfectly innocent – if an ass – John has a good, hard look at his motivations and what this galaxy is doing to him humanity. He’s not sure how he can change the path things are going down, though, not if they want to survive. How much is survival worth, if you lose everything that you are doing it?

And then there are sinking Jumpers (his babies. He has spaceships, an entire hangar full of them, to fly. There’s just nothing cooler than that, ever), and pseudo-medieval societies with – you guessed it – easy alien princesses. Bring on the Kirk jokes. John really doesn’t understand how these things keep happening to him (he never sees them coming), and he kind of wishes they wouldn’t. Because this time? She’s about sixteen, as far as he can tell. And he’s closing in on forty. And there are just so many ways in which that isn’t right, he doesn’t have time to list them all. He made the mistake of choosing a pretty little blonde once, and he isn’t about to do it again, thank you.

Then aliens are taking over his brain and making him try to kill Weir, and then he’s making a deal with the Genii again to get some of his people back, and then they’re testing a retrovirus on the Wraith to turn them human (and Texan, apparently), and then they’ve made some new friends and acquired and Ancient warship named Orion, and then there’re Wraith allies, and betrayals, and McKay and Ronon getting kidnapped, and testing stupidly unproven stunts in an F-302 while in hyperspace, and he just knows Rodney will kill him for that later. But there are explosions, and lots of Wraith, and they’ve lost the Orion and almost lost the Daedalus, but somehow they all make it back home, and then they’ve got to re-locate the humanized Wraith. Except this? Was not their best idea ever. He doesn’t know how this’ll turn out, but he’s just thankful Beckett is alive to see it, even though the security detail he left with the doc isn’t. Somewhere in there, too, there were awkward conversations with Teyla, and he’s thankful that she somehow seems to know what he meant to say when he stammered his way through telling her that she was important to him, because that’s not the sort of thing he’s good at. But she is, they all are, important to him that is. They’re the family he never expected to get back.

The common cold saves him after that, and it’s the first time he’s been grateful to it, although after he gets over the cold and has Rodney test Lucius’ herb on him, he’s in the disturbing position of being enamoured with his best friend. But that’s all right. Carson wields the needles, and normality is restored, just in time for them to run into some of Ronon’s past head-on. John learns more about the reticent alien than he ever thought he would, and it brings them all closer together, he thinks, but he wishes Ronon’s planet was still alive and that they’d never met, really, because Ronon deserves that. Then there are nano-something-or-others, and apparently that still means a lot more to just about everyone else, because John never served at the original SGC, and some things you just can’t really learn about by reading mission reports, no matter how thoroughly written (and Dr. Jackson’s were exceedingly thorough).

So they go back home, and Liz goes into a coma and John panics and paces because he’s supposed to protect these people, only he can’t protect them from their own minds, but he wishes he could. He needs something to attack, an enemy to stand against, and he hates it when there isn’t one. He hates being helpless. He always has, ever since he was fifteen and standing in a hospital waiting area.  
Speaking of helpless, the first time John becomes a prisoner of war, it’s to Kolya. And John really thinks he should’ve shot this guy when they first met, because he’s starting to get pretty damned annoying. But he’s a prisoner, being drained by a prisoner Wraith, and the only way they’re going to get out of the situation is if they work together. John’s studied tactics; he knows. So they form the most unlikely alliance ever (almost), and they get out, and then the Wraith drains him and John really thinks he’s made the biggest mistake ever and is going to die, except that suddenly he’s not, and the Wraith suddenly have a lot more dimensions than just ‘vampiric alien catfish’ to him. 

So John goes home to rest, and recover, and have Carson poke him with things, and fortunately things are quiet for a while. Well, except for McKay’s sister needing to come to Atlantis. That’s not quiet. She’s pretty, and brilliant, and John likes her immediately (probably because she reminds him of her brother, only a little softer around the edges), and watching them and how awkward Rodney is despite the fact that it’s clear he adores her, John thinks he understands his team-mate just a little bit better. So he sets out to do the best he can to patch up whatever rift is between them, by making sure Jeannie knows how much her brother’s done for earth, and how important he is to John’s city and everyone on it, and how much he loves her. He shows her the video Rodney recorded the first year they were there, and she’d never seen it before. Neither had John, actually; it’d just been hanging around on one of the old backups. But they both learn a bit from watching the ramblings of a Rodney who is exceptionally sleep deprived and high on stimulants and impending doom.

After Jeannie leaves, John is once again cleared for full duty, and the team heads back out, only to discover that the Genii have fucked with a Wraith research outpost. While trying to fix it, they start hallucinating, and if there’s one part of his life John never wanted to re-live? That was it. His team is surprisingly sympathetic – even McKay, after he gets over being shot – and it helps John a bit that now more people than just him know what happened, on that last mission in Afghanistan. A little bit. Not much. He really doesn’t think anything ever will help much.

So then John’s meeting his first living, breathing, un-Ascended Ancient, and they’re taking his city away from him. And that sucks. It sucks in so many ways he can’t even put words to. Life isn’t fair, though, John knows this. It’s just fairer than death. Wise words, from a movie most people probably don’t expect tough Air Force guys to watch. It’s one of John’s secret favorites. So they pack, and they go back to an earth that isn’t home anymore, and he’s put in charge of his own gate team at the SGC. And despite what everyone says about John’s team in Atlantis, these guys really make him wish for Rodney and Ronon and Teyla back. Because they suck. And it isn’t their fault, and it isn’t his, but the entire situation just sucks. He sees Rodney every so often for dinner, and Carson sometimes, but everyone else is scattered, and Liz won’t return his calls.

The second time John deliberately ignores a direct order, he knows exactly what it will cost him. He does it anyway, taking the Atlantis command team in a stolen jumper back into the Pegasus Galaxy to rescue their home from rogue replicators. Somehow, between Sam Carter’s guns and Rodney’s plotting and unexpected acting skills and everyone else being craftier than he’d ever guessed they could be, they get the city back and destroy the replicators while they’re at it. And the expedition team is recalled, and joy abounds in the city of the Ancients. Or so John says drunkenly to Rodney, during the party in the mess hall their first night back. John’s completely in shock that not only is he still in the Air Force, he’s still in command of Atlantis, but he vows then and there that he’ll never disobey an order again. Because this? Is too precious to play with. If he loses it, he’ll lose everything.

There are solar flares, and Lucius, and all manner of other pesky problems for a while. Although the Lucius problem is pretty much mitigated by the fact that John finally gets to shoot Kolya in a justified setting. He should probably feel worse about it than he does, but hey, he’ll be the first to admit that he’s not that good a man. Besides, Kolya was going to torture Rodney and Carson. Again. John can forgive a lot of things, but never that. He’s going to protect his people, no matter the cost. Of course, having determined that, it’s almost inevitable really that he almost loses Rodney, again, this time to yet another example of why the Ancients should have gone the way of the dodo long before they became the dominant species in two galaxies. John really, truly believes that Rodney’s going to die this time, especially when Rodney himself starts going around making his peace with people, so when he and Carson pull off another one of their off-the-wall miracles, John has to lock himself in his room for several hours. Because no one on the Atlantis mission really needs to see the head of military operations cry, and John doesn’t really want witnesses as he gets down on his knees and thanks a God he never believed in for the life of the man who has come to be the best friend he ever had.

So life goes on, and they almost destroy a pair of neighbouring civilizations because the Ancients need to leave freaking warnings on their experiments, dammit! (And okay, the destroying civilizations thing might also have had something to do with their own innate stubborn idiocy, but Liz doesn’t really need encouragement to call either of them – or their seconds – idiots, does she?) And then John’s pulling off the absolute worst landing he’s ever made, in a badly-damaged satellite moon thing that a race of people has built to try and escape the Wraith. John’s struck once again by the utter sameness of humanity – both the good and the bad – wherever he goes, in either galaxy. It’s something of a comfort, really, to know that there will always be petty people and people who put their families first and people who love and people who hate, somewhere in the galaxy.

John’s tired after this, they all are, really, and he’s more than grateful when Kate Heightmeyer orders mandatory downtime one Sunday. He takes it gratefully, only grumbling a little bit when his lounging with Ronon (after the man kicks his ass a few times) is interrupted by an explosion in one of the panels near the mess hall. But he’s back in his quarters when McKay stops by that night, after the circuit panels are dealt with, with a shocked look in his eyes and the news that Carson’s going. They both turn out to watch their friend step through the wormhole, and John’s long since perfected the poker face that conceals how much he cares for people when they’re leaving him, but this time he drops it. Because this time, he doesn’t have to hide that he’s going to miss his friend terribly.


End file.
